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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on Aug 23, 2007
*
*/
package org.biojava.bio.alignment;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
import org.biojava.bio.seq.io.SymbolTokenization;
import org.biojava.bio.symbol.Alphabet;
import org.biojava.bio.symbol.AlphabetManager;
import org.biojava.bio.symbol.FiniteAlphabet;
import org.biojava.bio.symbol.Symbol;
import junit.framework.TestCase;
public class SubstitutionMatrixTest extends TestCase {
public void testParseSubstitutionMatrix(){
InputStream inStream = this.getClass().getResourceAsStream("/files/blosum62.mat");
assertNotNull(inStream);
try {
FiniteAlphabet alphabet = (FiniteAlphabet) AlphabetManager.alphabetForName("PROTEIN-TERM");
SymbolTokenization symtok = alphabet.getTokenization("token");
//String file = readMatrix(inStream);
//SubstitutionMatrix matrix = new SubstitutionMatrix(alphabet,file,"blosum 62");
SubstitutionMatrix matrix = SubstitutionMatrix.getSubstitutionMatrix(
new BufferedReader(new InputStreamReader(inStream)));
//matrix.printMatrix();
Symbol A = symtok.parseToken("A");
Symbol W = symtok.parseToken("W");
Symbol D = symtok.parseToken("D");
assertEquals(matrix.getValueAt(A, A), 4);
assertEquals(matrix.getValueAt(W, D),-4);
} catch (Exception e){
fail(e.getMessage());
}
}
private String readMatrix(InputStream stream) throws IOException{
String newline = System.getProperty("line.separator");
BufferedReader reader = new BufferedReader(new InputStreamReader( stream));
StringBuffer file = new StringBuffer();
while (reader.ready()){
file.append(reader.readLine() );
file.append(newline);
}
return file.toString();
}
}
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